MSAview: A Tool to Highlight Distant Interactions among Amino Acid Residues using Sequence Alignment

Abstract

Within this thesis a standalone application “MSAview” has been developed to highlight distant interactions among key amino acid residues by adding a layer of information over the existing multiple sequence alignment (MSA) analysis. This tool has been developed within the framework of sequence alignment results and associated protein structures. It extracts the structural information from protein reference structure and maps it to the sequence alignment to highlight distant interactions among the amino acid residues present at a distant of 5 Å. Furthermore, MSAview has been used for the prediction of key amino acid residues and their intermolecular interactions within the binding pocket of target protein. It was validated by using White box, Black box testing, and on Balibase workbench however; a direct correlation between % sequence identity and accuracy of the predicted interactions between key amino acid resides has been identified. The developed tool could pave the way for web based protein fold prediction and analysis after triumphing of some major limitations.